No. It doesn't change anything if the size is in the PDF header. The size of both PDFs are the same, the header of both PDF files is the same on the both "shattered" files now.
What Linus says is that if you tried to put these two PDF files in git, it would not see them as the same, as git calculates the sha1 differently. But Google would be able to produce two PDF files that would, as git sees them, appear to be same just as easy as these that were produced.
P.S. (answer to your answer to this message) Note, You wrote one level above
> If PDF had a header at the beginning of the file that states the file size, then it could be harder to find a collision.
And I argued that it isn't harder, but irrelevant.
From your answer:
> But to generate a collision with a different prefix q one would have to do the expensive computation all over again
Yes. Now read what your claim was again. It's not harder. Exactly as easy as the first time.